Arabidopsis Research Roundup: August 27th

The Arabdopsis Research Roundup broadens its remit this week. As well as including three original research papers, which look at casparian strip formation, light and hormone signaling, we also highlight an important viewpoint article that aims to set standards for synthetic biology parts. In addition we include a meeting report from a plant synthetic biology summer school and interviews with plant scientists at the JIC, Caroline Dean and Anne Osbourn.

Kamiya T, Borghi M, Wang P, Danku JM, Kalmbach L, Hosmani PS, Naseer S, Fujiwara T, Geldner N, Salt DE (2015) The MYB36 transcription factor orchestrates Casparian strip formation Proc Natl Acad Sci USA Open Access

GARNet Advisory Board Chairman David Salt (Aberdeen) leads this international collaboration that looks at the (relatively) poorly understood Casparian strip (CS), a lignin-based filter that lies in root endodermal cells. Formation of the CS is initiated by Casparian strip domain proteins (CASPs) that recruit other proteins, which begin the process of lignin deposition. In this study the authors look upstream this process and identify the transcription factor MYB36 that directly regulates expression of CASPs and is essential for CS formation. Ectopic expression of MYB36 in root cortical tissues is sufficient to stimulate expression of CASP1-GFP and subsequent deposit a CS-like structure in the cell wall of cortex cells. These results have implications for the design of future experiments that aim to control how nutrients are taken up by the plant as even though myb36 mutants have a ‘root-defect’, they also have changes to their leaf ionome.

Sadanandom A, Ádám É, Orosa B, Viczián A, Klose C, Zhang C, Josse EM, Kozma-Bognár L, Nagy F (2015) SUMOylation of phytochrome-B negatively regulates light-induced signaling in Arabidopsis thaliana Proc Natl Acad Sci USA Open Access

Ari Sadanandom (Durham) and Ferenc Nagy (Edinburgh) are the leaders of this study that investigates the precise function of the PhyB photoreceptor protein. PhyB interacts with a wide range of downstream signaling partners including the PHYTOCHROME INTERACTING FACTOR (PIF) transcription factors. The small ubiquitin-like modifier (SUMO) peptide is conjugated to larger proteins to bring about a variety of signaling outcomes. In this case the authors find that SUMO is preferentially attached to the C-term of PhyB under red light conditions, a relationship that occurs in a diurnal pattern. SUMOylation of PhyB prevents interaction with PIF5 whilst the OVERLY TOLERANT TO SALT 1 (OTS1) protein likely de-SUMOlyates PhyB in vivo. Altered levels of PhyB SUMOylation cause distinct light-responsive phenotypes and as such this paper adds another level of regulation to the already complex known network that controls light signaling.

Schuster C, Gaillochet C, Lohmann JU (2015) Arabidopsis HECATE genes function in phytohormone control during gynoecium development Development. Open Access

Christopher Schuster who is now a postdoc based at the Sainsbury lab in Cambridge is the lead author on this investigation into the role of the HECATE (HEC) family of bHLH transcription factors on fruit development in Arabidopsis. During this process HEC proteins are involved in the response to both the phytohormones auxin and cytokinin, the authors proposing that HEC1 plays an essential role in Arabidopsis gynoecium formation.

Patron N et al (2015) Standards for plant synthetic biology: a common syntax for exchange of DNA parts New Phytologist Open Access

Carmichael RE, Boyce A, Matthewman C Patron N (2015) An introduction to synthetic biology in plant systems New Phytologist Open Access

Although not strictly based on Arabdopsis work, there are a couple of articles in New Phytologist that have broad relevance to plant scientists who are interested in plant synthetic biology. In the first of these Nicola Patron (The Sainsbury Laboratory) leads a wide consortium that aims to set parameters for the standardisation of parts in plant synthetic biology. It is hoped that as the principles of synbio are used more widley in the plant sciences that the proposals in this paper will serve as a useful guide to standidise part production. GARNet has recently written a blog post on this topic.
The associated meeting report looks at the use of plant synthetic biology in a teaching context with a synopsis of the ERASynBio summer school hosted by John Innes Centre. In this event, young researchers from a range of backgrounds were introduced to the power and potential of plant synthetic biology through a diverse course of lectures, practical session and group projects.


Vicente C (2015) An interview with Caroline Dean Development Open Access

An interview with Anne Osbourn (2015) New Phytologist <a href="http://dx.doi acheter″ onclick=”_gaq.push([‘_trackEvent’, ‘outbound-article’, ‘’, ‘ ‘]);” target=”_blank”> Open Access

These are interviews with eminent female plant molecular biologists who both work at the John Innes Centre. Caroline Dean’s lab focuses on the epigenetic mechanisms that regulate vernalisation whilst Anne Osbourn is interested in using synthetic biology approaches to engineer metabolic pathways for the production of novel compounds.

Arabidopsis Research Roundup: July 30th

Two broad topics dominant the studies featured in this weeks Arabidopsis Research Roundup. Environmental and hormonal factors that control different types of ‘dormancy’ are presented in studies from the labs of Caroline Dean (JIC) and Ian Graham (York). Elsewhere two Sainsbury lab (Norwich) led studies investigate different aspects of the interaction between plants and bacterial pathogens. Finally Colin Turnbull from Imperial College is involved in an interesting assessment of cytokinin concentrations across the root tip.

Duncan S, Holm S, Questa J, Irwin J, Grant A, Dean C (2015) Seasonal shift in timing of vernalization as an adaptation to extreme winter Elife.

Caroline Dean (JIC) again publishes in the open access journal eLife as her lab continues to investigate the precise detail of the vernalisation response. This response shows natural variation that is dependent on the geographic distribution of Arabidopsis ecotypes. Plants collected from northern latitudes showed maximum vernalisaton at 8oC, both at the level of flowering time and FLC chromatin silencing. The vernalisation response was measured both in controlled and field conditions and all Northern ecotypes were importantly shown to vernalise prior to snowfall, which would allow flowering immediately after thawing. These findings have important implications for models aimed at predicting the affect of climate change on flowering time.

Ibarra SE1, Tognacca RS1, Dave A2, Graham IA2, Sánchez RA1, Botto JF (2015) Molecular mechanisms underlying the entrance in secondary dormancy of Arabidopsis seeds Plant Cell Environ

Ian Graham is the leader of the Centre for Novel Agricultural Products (CNAP) at the University of York and contributes to this Argentinian-led study that looks into the molecular factors that underlie secondary dormancy in Arabidopsis seeds. They show that this process involves changes in the content and sensitivity to GA (but not ABA) that requires the activity of the RGL2 protein acting through ABI5. A wide geographical study then perhaps unsurprisingly showed that temperature is also an important variable influencing the induction of secondary dormancy

Lee D, Bourdais G, Yu G, Robatzek S, Coaker G (2015) Phosphorylation of the Plant Immune Regulator RPM1-INTERACTING PROTEIN4 Enhances Plant Plasma Membrane H+-ATPase Activity and Inhibits Flagellin-Triggered Immune Responses in Arabidopsis Plant Cell

Silke Robatek (TSL) is the UK lead on this collaboration with UC-Davis that looks at phosphorylation of RPM1-INTERACTING PROTEIN4 (RIN4) in a range of Arabidopsis genotypes that are suspectible to infection. Flexibility of the RIN4 protein is affected by phosphorylation and this causes enhanced suspectibility coincident with increasing plasma membrane H+-ATPase activity. The expression of the AHA1 ATPase is high in guard cells and therefore linked to stomatal opening. As such bacterial infection works to phosphorylate RIN4 that in turn increases the chance of bacterial entry.

Pfeilmeier S, Saur IM, Rathjen JP, Zipfel C, Malone JG (2015) High levels of cyclic-di-GMP in plant-associated Pseudomonas correlate with evasion of plant immunity Mol Plant Pathology

GARNet Advisory Board Member Cyril Zipfel (TSL) and Jacob Malone (JIC) investigate the response to pathogen/microbe-associated molecular patterns (PAMPs/MAMPs) by the plant innate immune system. The resulting pattern-triggered immunity (PTI) fends off pathogen attack by recognition of bacterial flagellin by, amongst others, the FLAGELLIN SENSING2 (FLS2) protein. In this study the authors focus on the bacterial side of the response and show that cyclic-di-GMP is involved in the evasion of PTI, although this also reduces virulence, likely due to reduced flagellar motility. This results in a trade off for the bacteria in which it is not recognised as readily by plant yet isn’t as virulent.

Antoniadi I, Plačková L, Simonovik B, Doležal K, Turnbull C, Ljung K, Novák O (2015) Cell-Type-Specific Cytokinin Distribution within the Arabidopsis Primary Root Apex Plant Cell

Colin Turnbull (Imperial College) is a contributor to this Swedish-Czech collaboration that measures cytokinin concentrations in root cell files isolated by FACS and analysed by MS. The authors show a gradient of cytokinin across the root tip with maximum concentrations in the lateral root cap, columnella and QC cells. As these are also areas of high auxin concentration, the authors suggest that this implies that interactions between the two hormone groups are cell type specific.

Arabidopsis Research Roundup: July 20th

There is a bumper crop of publications in high quality journals in this weeks UK Arabidopsis Research Roundup, including manuscripts in PNAS, Nature Communications, PLoS Genetics , PloS One and Plant Physiology. Malcolm Bennett, Alex Webb and Anthony Hall lead a major collaborative effort that links the circadian clock with lateral root formation whilst Ottoline Leyser (SLCU) and Mike Bevan (JIC) participate in a similarly broad consortium in a study linking organ size and MAPK signaling. Liam Dolan’s group from Oxford looks at mechanisms of tip-growth across the plant kingdoms whilst elsewhere three members of faculty at the University of Birmingham are involved in two papers looking at the regulation of meiosis. Finally there are two US-led studies that include significant contributions from UK-based researchers, including Matthew Jones from the University of Essex.


Voß U, Wilson MH, Kenobi K, Gould PD, Robertson FC, Peer WA, Lucas M, Swarup K, Casimiro I, Holman TJ, Wells DM, Péret B, Goh T, Fukaki H, Hodgman TC, Laplaze L, Halliday KJ, Ljung K, Murphy AS, Hall AJ, Webb AA, Bennett MJ (2015) The circadian clock rephases during lateral root organ initiation in Arabidopsis thaliana Nature Communication 6:7641.

Once again Malcolm Bennett (CPIB) leads a multi-Institute collaboration that includes Alex Webb (Cambridge) and current GARNet board member Anthony Hall (Liverpool). This is also an extremely international effect with groups from the UK, USA, Sweden, Japan, Spain and France. The science looks at lateral root stems cells and how the circadian clock is rephased during LR emergence. They show that the clock controls auxin levels and auxin-related genes. The conclusion is that the circadian clock acts to gate auxin signalling during LR development to facilitate organ emergence and adds to a growing portfolio of evidence that suggest the circadian clock might act in a cell autonomous manner. Anthony Hall, James Locke and Peter Gould currently have a grant that is looking at this phenomenon in Arabidopsis root cells.


Johnson KL, Ramm S, Kappel C, Ward S, Leyser O, Sakamoto T, Kurata T, Bevan MW, Lenhard M (2015) The Tinkerbell (Tink) Mutation Identifies the Dual-Specificity MAPK Phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) as a Novel Regulator of Organ Size in Arabidopsis PLoS One.10(7):e0131103.

Ottoline Leyser, Sally Ward (Sainsbury lab, Cambridge) and Mike Bevan (JIC) are the UK contributors to this joint UK-German-Japanese-Australian collaboration. This study follows a screen for plants with reduced organ size and introduces a novel allele of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5), named Tinkerbell (tink). This mutation reveals that IBR5 is a novel regulator of organ size by changing the growth rate in petals and leaves although this occurs independent of the previously characterised KLU pathway. The authors use microarray data to suggest an additional role for TINK/IBR5 during male gametophyte development. Ultimately they conclude that IBR5 might influence organ size through auxin and TCP growth regulatory pathways.


Tam TH, Catarino B, Dolan L (2015) Conserved regulatory mechanism controls the development of cells with rooting functions in land plants Proc Natl Acad Sci U S A.

Liam Dolan’s lab at the University of Oxford is a world leader in the study of root hair development. Previously it has been shown the group XI basic helix-loop-helix (bHLH) transcription factor (LOTUS JAPONICUS ROOTHAIRLESS1-LIKE (LRL) regulates root hair growth in Arabidopsis, Lotus or rice. This study investigates the equivalent proteins in the moss Phycomitrella patens and show that they are involved in an auxin signaling pathway that promotes cell outgrowth albeit via a different set of signaling intermediates. Overall the authors show that a core auxin network that supports cellular ‘tip-growth’ exists throughout land plant lineages even though the specificity of this signaling has diverged over the course of the ~420million years that separates angiosperms and mosses.


Varas J, Sánchez-Morán E, Copenhaver GP, Santos JL, Pradillo M (2015) Analysis of the Relationships between DNA Double-Strand Breaks, Synaptonemal Complex and Crossovers Using the Atfas1-4 Mutant. PLoS Genet.11(7): e1005301.

The work led by Monica Pradillo at the University of Madrid includes a contribution from Eugenio Sanchez-Moran from the University of Birmingham. This work focuses on the hetero-trimeric Chromatin Assembly Factor 1 (CAF-1), which is a histone chaperone that assembles acetylated histones H3/H4 onto newly synthesized DNA. In Arabidopsis the CAF1 complex is composed of the FAS1, FAS2 and MSI1 proteins. Atfas1 mutant plants are less fertility, have a higher number of double stranded breaks (DSB) and show a higher gene conversion frequency. The authors investigate how DSBs can influence meiotic recombination and synaptonemal complex (SC) formation by genetic analysis of Atfas1-containing double mutants. Ultimately their experiments provide new insights into the relationships between different recombinase proteins in Arabidopsis. Overall an increase in the number of DSBs does not translate to an increase in the number of crossovers (COs) but instead in a higher GC frequency. The authors provide different theories to explain this mechanism, including the possible existence of CO homeostasis in plants.


Lambing C, Osman K, Nuntasoontorn K, West A, Higgins JD, Copenhaver GP, Yang J, Armstrong SJ, Mechtler K, Roitinger E, Franklin FC (2015) Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers PLoS Genetics 11(7):e1005372

The University of Birmingham is the lead Instiution in this study that also investigates regulation of meiosis. The groups of Chris Franklin and Sue Armstrong collaborate with US and Austrian partners to study the organization of meiotic chromosomes during prophase I. Using structured illumination microscopy (SIM) they show that dynamic changes in chromosome axis is coincident with synaptonemal complex (SC) formation and depletion of the ASY1 protein, which requires the function of the PCH2 ATPase. Using a pch2 mutant the authors are able to tease apart different aspects of ‘crossover’ (CO) biology and that the pch2 defect occurs precisely during CO maturation, not during designation. In addition, CO distribution is also affected in some chromosome regions showing that failure to deplete ASY1 can result in downstream events that include disruption of CO patterning.


Jones MA, Hu W, Litthauer S, Lagarias JC, Harmer S (2015) A Constitutively Active Allele of Phytochrome B Maintains Circadian Robustness in the Absence of Light Plant Physiology.

Matthew Jones (University of Essex) is the primary author of this work that comes from a collaboration from his time in the lab of Stacey Harmer in UC Davis. Since 2012 Matthew has been a lecturer at the University of Essex where he continues with work of this nature. In this study they introduce a constitutively active allele of the PHYB photoreceptor that is able to phenoopy red-light input into the circadian clock. In these mutants the pace of the clock is insensitive to light-intensity and this response is dependant on its PHYB nuclear localisation. Finally they show that fine tuning of PHYB signalling requires PHYC and overall they conclude that nuclear phytocrome signalling is necessary for sustaining clock function under red light.


Chakravorty D, Gookin TE, Milner M, Yu Y, Assmann SM (2015) Extra-Large G proteins (XLGs) expand the repertoire of subunits in Arabidopsis heterotrimeric G protein signalling Plant Physiol.

Sally Assman from Penn State University leads this study that includes a contribution from Matthew Milner who now works at NIAB. The number of proposed G protein subunits is greatly reduced in diploid plant genomes yet this study shows that a family of Arabidopsis GPA-related proteins (XLG1-3) can increase the repertoire of potential G proteins interactions by interacting with beta and gamma subunits. The authors propose they have uncovered a new plant-specific paradigm in cell signaling.

Arabidopsis Research Roundup: June 10th.

This weeks UK Arabidopsis Research Roundup features work from two members of the GARNet advisory board who are working on very different aspects of how plants response to external stimuli. In addition there is a genetic and biochemical dissection of primary cell wall formation as well as a comment piece that questions recent findings concerning the relationship between auxin, ABP1 and cortical microtubules.

Busoms S, Teres J, Huang X, Bomblies K, Danku J, Douglas A, Weigel D, Poschenrieder C, Salt DE (2015) Salinity is an agent of divergent selection driving local adaptation of Arabidopsis thaliana to coastal habitats Plant Physiology

Current GARNet Chairman David Salt from Aberdeen has collaborated with researchers from Spain, Germany and the USA in this study that looks at the drivers of adaptive evolution of Arabidopsis plants grown in saline conditions. Unusually this is a field-based study using Arabidopsis that naturally grow in coastal or inland areas of NE Span. Plants taken from coastal areas outperform inland plants when grown on highly saline soils, indicating local adaptation to salt tolerance. The authors conclude that the variation in sodium concentration is causing divergent selection between these two populations.

Monaghan J, Matschi S, Romeis T, Zipfel C (2015) The calcium-dependent protein kinase CPK28 negatively regulates the BIK1-mediated PAMP-induced calcium burst Plant Signaling and Behaviour June 2015

GARNet advisory board member Cyril Zipfel from the Sainsbury lab led this study looking at the role of the cytoplasmic kinase BIK1 in the plants response to microbial infection. In plants that are mutant for the Ca2+-dependent protein kinase CPK28, BIK1 accumulates, which leads to enhancing immune signaling. In this study the authors add to these previous finding from their lab by showing that CPK28 also contributes to a burst of Ca2+ production following exposure to pathogens.

Mortimer JC, Faria-Blanc N, Yu X, Tryfona T, Sorieul M, Ng YZ, Zhang Z, Stott K, Anders N, Dupree P (2015) An unusual xylan in Arabidopsis primary cell walls is synthesised by GUX3, IRX9L, IRX10L and IRX14 Plant Journal

Paul Dupree from the Biochemistry department at the University of Cambridge led this work that investigated a newly characterised form of Xylan, a little studied component of the plant primary cell wall. Genetic analysis indicates that the IRX9L, IRX10L and IRX14 proteins are necessary for xylan backbone synthesis. Importantly this new xylan is contains GlcA side chains, whose addition only requires the glucuronyltransferase GUX3. This type of xylan has not been observed in secondary cell walls so the authors comment on how differences in xylan structure assist in the formation of primary vs secondary cell walls.

Taken from wikipedia.
Taken from wikipedia.






T Baskin (2015) Auxin inhibits expansion rate independently of cortical microtubules. Trends in Plant Science

Visiting scholar at CPIB in Nottingham, Tobias Baskin provides a short reply to a publication in Nature that claimed that the control of cell expansion by auxin is caused by reorientation of cortical microtubules. In this paper, Tobias provides evidence from both a simple experiment and from the literature that this might not be the paradigm-shifting observation that it initially appears.

Arabidopsis Research Roundup: May 27th

This weeks Arabidopsis Research Roundup sees a small number of high quality publications driven by UK-based researchers together with a couple of collaborative efforts that highlight the international aspect of research. Topics include two greatly different descriptions of how a plant responds to attack, an investigation into the intersection of vesicle and potassium transport as well as descriptions of auxin and sugar signaling.

Sarris PF, Duxbury Z, Huh SU, Ma Y, Segonzac C, Sklenar J, Derbyshire P, Cevik V, Rallapalli G, Saucet SB, Wirthmueller L, Menke FL, Sohn KH, Jones JD (2015) A Plant Immune Receptor Detects Pathogen Effectors that Target WRKY Transcription Factors. Cell 161, p1089-1100

Jonathan Jones at the Sainsbury lab collaborated with his ex-PhD student Kee Hoon Sohn (now at Massey University in NZ) to produce this high profile publication in Cell. Professor Jones’s group has been in the vanguard of research into the response to bacterial pathogens and this paper adds a further layer of understanding as they show that the plant uses a bacteria’s own ‘attack mechanism’ against itself. Many bacterial effector proteins target WRKY DNA-binding protein domains in order to interfere with transcription. This work shows that the plant defence factor RRS1 also contains a WRKY domain, enabling it to ‘sense’ when the bacteria is in the cell and act as a decoy that makes the bacteria subsequently open to attack.


Jaouannet M, Morris JA, Hedley PE, Bos JI (2015) Characterization of Arabidopsis Transcriptional Responses to Different Aphid Species Reveals Genes that Contribute to Host Susceptibility and Non-host Resistance. PLos Pathogens 11: e1004918.

The group of Jorunn Bos at the James Hutton Institute in Dundee looked at a different aspect of the defence response whereby they investigated transcriptional responses to aphid predation on Arabidopsis. Host and non-host responses to aphids show a high degree of overlap in expression but interestingly the host response included repressive of genes involved in metabolism and oxidative response. This type of study will pave the way for the future development of aphid control strategies in crop plants and once again highlights the utility of Arabidopsis as a model system.


Zhang B, Karnik R, Wang Y, Wallmeroth N, Blatt MR, Grefen C (2015) The Arabidopsis R-SNARE VAMP721 Interacts with KAT1 and KC1 K+ Channels to Moderate K+ Current at the Plasma Membrane Plant Cell [Epub]

Control of potassium channels is the focus of this work from Mike Blatt’s lab at the University of Glasgow. They identify a subset of SNARE proteins (that are involved in vesicle trafficing) that control K+ channels, albeit in an unconventional manner. The vesicle-associated membrane proteins 721 (VAMP721) is able to target vesicles as well as supressing the actitivty of the K+ channels KAT1 and KC. This leads to a model whereby different subsets of SNARE proteins opposingly effect K+ channel activity alongside having an effect on vesicular transport.


Panoli A, Martin MV, Alandete-Saez M, Simon M, Neff C, Swarup R, Bellido A, Yuan L, Pagnussat GC, Sundaresan V. (2015) Auxin Import and Local Auxin Biosynthesis Are Required for Mitotic Divisions, Cell Expansion and Cell Specification during Female Gametophyte Development in Arabidopsis thaliana. PLoS One. 10:e0126164.

The primary interest of Ranjan Swarup’s group at the University of Nottingham is in hormone signalling and root development yet he is included as a collaborator in this publication led from UC-Davies that focusses on auxin signalling during female gametophyte development. The paper shows that the YUCCA family of the auxin biosynthetic genes are asymmetrically expressed during embryo sac development and that the AUX1 and LAX1 auxin influx carriers are expressed only at both the micropylar pole of the embryo sac and in adjacent cells of the ovule. In addition aux1lax1lax2 triple mutants show numerous gametophytic developmental defects.  Given the importance of auxin in most aspects of plant development, this paper highlights the specific manner in which auxin is required for mitotic divisions, cell expansion and patterning during embryo sac development.


Zheng L, Shang L, Chen X, Zhang L, Xia Y, Smith C, Bevan MW, Li Y, Jing HC (2015) TANG, Encoding a Symplekin_C Domain-contained Protein, Influences Sugar Responses in Arabidopsis Plant Physiol [Epub]

Mike Bevan at the JIC is a collaborator on this Chinese driven project that investigates Arabidopsis tang1 mutants. These plants are hypersensitive to sugar amd following a classic map-based cloning approach, the TANG1 gene was found to encode a novel protein with a predicted Symplekin tight junction protein C-terminal. As TANG1 is ubquitiously expressed and has little effect on known sugar signalling pathways, the precise in vivo role of the protein remains somewhat opaque even though it is clearly an important player in the response to sugar in Arabidopsis.

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